1HKD

Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2LTNPDB ENTRY 2LTN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.7 M AMMONIUM SULFATE, 10% (V/V) ETHANOL, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
1.9436.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.793α = 90
b = 61.235β = 90
c = 136.005γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHMIRRORS2002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEELLIOTT GX-6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123095.40.05817.92.83000528.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0383.50.421.922.19

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2LTN2.0927.9523508118198.30.1650.1630.209RANDOM22.77
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.46-0.09-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.794
r_dihedral_angle_1_deg2.936
r_scbond_it2.532
r_mcangle_it1.867
r_angle_refined_deg1.305
r_mcbond_it1.02
r_nbd_refined0.235
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.794
r_dihedral_angle_1_deg2.936
r_scbond_it2.532
r_mcangle_it1.867
r_angle_refined_deg1.305
r_mcbond_it1.02
r_nbd_refined0.235
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.141
r_chiral_restr0.1
r_metal_ion_refined0.068
r_gen_planes_refined0.01
r_bond_refined_d0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3576
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing